Align Aromatic-amino-acid aminotransferase 1; ARAT-I; AROAT; EC 2.6.1.57 (characterized)
to candidate 8502295 DvMF_3003 putative transcriptional regulator, GntR family (RefSeq)
Query= SwissProt::H3ZPL1 (417 letters) >FitnessBrowser__Miya:8502295 Length = 394 Score = 314 bits (804), Expect = 3e-90 Identities = 162/389 (41%), Positives = 244/389 (62%), Gaps = 16/389 (4%) Query: 32 SEIRELLKLVETSDVISLAGGLPAPETFPVEIIGEITKEVLEKHAAQALQYGTTKGFTPL 91 S IRE+LK+ D+IS AGGLP P +FPV+ + VLE+ +ALQY TT+GF PL Sbjct: 13 SYIREILKVTAQPDIISFAGGLPHPASFPVDAVASAAASVLEEAGPEALQYTTTEGFPPL 72 Query: 92 RLALAEWMRERYD---IPISKVDIMTTSGSQQALDLIGRVFINPGDIIVVEAPTYLAALQ 148 R +W+ +RY I +S DI+ T+GSQQALDL+ + I+ G +V+E P YL A+Q Sbjct: 73 R----QWIADRYKRQGINVSPDDILITTGSQQALDLVAKACIDRGGRVVMERPGYLGAIQ 128 Query: 149 AFKYYEPEFVQIPLDDEGMNVDLLEEKLQELEKEGKKVKIVYTIPTFQNPAGVTMNEKRR 208 F + P+FV +PL G++ D L K ++ Y +P+FQNP+G+T +E+ R Sbjct: 129 CFSVFGPDFVTVPLTPRGVDTDALR-------KAATGAQVFYAVPSFQNPSGITYDEQTR 181 Query: 209 KRLLELASQYDFIIVEDNPYGELRYSGEPVKPIKAWDEEGRVIYLGTFSKILAPGFRIGW 268 + + E+ ++ ++VEDNPYGELR+ G+ + P++A+ + V+ LG+FSK+++PG R+GW Sbjct: 182 REVAEIMAETGCLMVEDNPYGELRFMGQHLPPVRAYMQAPSVL-LGSFSKVVSPGLRLGW 240 Query: 269 IAAEPHFIRKLEIAKQSVDLCTNTFSQVIAWKYVEGGYLDKHIPKIIEFYKPRRDAMLKA 328 + A + + AKQ+ DL T F+Q I +Y+ +DKHI I Y +RDAM++A Sbjct: 241 VCAPQEVLNPMITAKQASDLHTPGFTQRILHRYLMDNDVDKHIASIRARYGAQRDAMVQA 300 Query: 329 LEEFMPDGVKWTKPEGGMFVWATLPEGIDTKLMLEKAVAKGVAYVPGEAFFAHRDVKNTM 388 + P+ V T+PEGGMF+W TLPEGI + + KA+ + VA+VPG F+ + +T Sbjct: 301 IRRHFPEDVACTEPEGGMFLWCTLPEGISAEALFHKAIERKVAFVPGRPFYVD-ETDDTF 359 Query: 389 RLNFTYVPEEKIREGIKRLAETIKEEMKK 417 RLNF+ E I EGI RL + ++E + K Sbjct: 360 RLNFSNSSPELIEEGIARLGQCLREYLGK 388 Lambda K H 0.318 0.137 0.398 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 459 Number of extensions: 24 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 417 Length of database: 394 Length adjustment: 31 Effective length of query: 386 Effective length of database: 363 Effective search space: 140118 Effective search space used: 140118 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory